Re: [Seqan-dev] razers3 "failed for left reads in thread"

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

Dear Nomi, can you provide the files to us (contact me privately if you don't want to share the data)?

In the meantime, you could try to use "-tc 0" which uses the non-parallel code path instead of the parallel one (-tc 1 would call the parallel code path with one thread).

It appears that you are running against genes, i.e. many small sequences, which might be a less well-trodden path in RazerS and thus mit require a fix. We'd be happy to help and the best way would be to provide us with the reference and the reads (privately if you prefer) so we can reproduce your error. If possible, it would be great, if you could reduce your dataset, e.g. to some hundred references and reads, as long as you still get the same problem. Often, it is possible to reduce the dataset below a few MB of data.

Cheers,
Manuel
________________________________________
From: Nomi Meixner [nomi.meixner@student.uni-tuebingen.de]
Sent: Monday, July 22, 2013 12:27 PM
To: SeqAn Mailing list
Subject: [Seqan-dev] razers3 "failed for left reads in thread"

Dear all,

I've installed the latest svn version of SeqAn on Scientific Linux. I
tried several compilers. Latest try were Intel 12.0 and Gnu 4.4.

Running the following command failed on all versions (though mentioned
files were present):
razers3 -tc 4 -o reference.sam mass_timo_ccug_45783.1.genes.fasta
GS120675_03_CGATGT_L001_R1_001.fastq GS120675_03_CGATGT_L001_R2_001.fastq

However a colleague was able to run razers3 on those files on his Ubuntu
machine a while ago, probably not with the latest version!

The error looks the following on the gnu-compiled version:
ERROR: windowFindBegin() failed for left reads in thread ERROR:
windowFindBegin() failed for left reads in thread ERROR:
windowFindBegin() failed for left reads in thread ERROR:
windowFindBegin() failed for left reads in thread 1230



ERROR: windowFindBegin() failed for right reads in thread 2
ERROR: windowFindBegin() failed for right reads in thread 3
ERROR: windowFindBegin() failed for right reads in thread 1
ERROR: windowFindBegin() failed for right reads in thread 0
ERROR: windowFindBegin() failed for left reads in thread ERROR:
windowFindBegin() failed for left reads in thread ERROR:
windowFindBegin() failed for left reads in thread ERROR:
windowFindBegin() failed for left reads in thread 0
321ERROR: windowFindBegin() failed for right reads in thread 0

ERROR: windowFindBegin() failed for right reads in thread 1


ERROR: windowFindBegin() failed for right reads in thread 3
ERROR: windowFindBegin() failed for right reads in thread 2
ERROR: windowFindBegin() failed for left reads in thread ERROR:
windowFindBegin() failed for left reads in thread ERROR:
windowFindBegin() failed for left reads in thread ERROR:
windowFindBegin() failed for left reads in thread 0132
ERROR: windowFindBegin() failed for right reads in thread 0

ERROR: windowFindBegin() failed for right reads in thread 1

ERROR: windowFindBegin() failed for right reads in thread 2

ERROR: windowFindBegin() failed for right reads in thread 3
ERROR: windowFindBegin() failed for left reads in thread ERROR:
windowFindBegin() failed for left reads in thread ERROR:
windowFindBegin() failed for left reads in thread ERROR:
windowFindBegin() failed for left reads in thread 01
ERROR: windowFindBegin() failed for right reads in thread 1



It continues like this and terminated with a segmentation fault. The
messages on the intel-compiled version look pretty much the same.

Except for the SeqAn source code I couldn't find anything about this
issue on the web. To get clues from the source code, my knowledge about
SeqAn is far too superficial.

I would be glad if someone could tell me what is going wrong here and
how to tackle this issue.

Thank you very much in advance!
All the best,
Nomi

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